ArticleCell2023
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.
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In one paragraph
Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
55citing papers in PubMed, 2 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genetic drivers of etiologic heterogeneity in thyroid cancer.Nature communications · 2026Pooled it
- Investigating the shared genetic information between serum concentration levels of liver enzymes and cholelithiasis.BMC gastroenterology · 2025Pooled it
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.Cell genomics · 2026Article
- Human body single-cell atlas of three-dimensional genome organization and DNA methylation.Science (New York, N.Y.) · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Epigenetic characterization of pseudogenes across human tissues.Genome research · 2026Article
- Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants.American journal of human genetics · 2026Article
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
- Aggregation of gene regulatory information and knowledge on FAIR principles enables discovery of pathogenic gene regulatory variants.Bioinformatics (Oxford, England) · 2026Article
- Towards personalized epigenomics: learning shared chromatin landscapes and joint de-noising of histone modification assays.NAR genomics and bioinformatics · 2025Article
- A multi-omics molecular landscape of 30 tissues in aging female rhesus macaques.Nature methods · 2025Article
- A combined genomic arrhythmia propensity score delineates cumulative risk.Cell reports. Medicine · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.Nucleic acids research · 2025Article
- Genetics-nutrition interactions control diurnal enhancer-promoter dynamics and liver lipid metabolism.Cell metabolism · 2025Article
- Regulatory genome annotation.Nature reviews. Genetics · 2025Article
- Patterns of extreme outlier gene expression suggest an edge of chaos effect in transcriptomic networks.Genome biology · 2025Article
Corrections and comments
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Authors and funding
103 authors.
Joel RozowskySection on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Jiahao GaoProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Beatrice BorsariProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Yucheng T YangInstitute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Timur GaleevProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Gamze GürsoyProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Charles B EpsteinBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kun XiongProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Jinrui XuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Tianxiao LiProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Jason LiuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Keyang YuDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Ana BerthelProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Zhanlin ChenDepartment of Statistics and Data Science, Yale University, New Haven, CT, USA.
Fabio NavarroProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Maxwell S SunProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
James WrightInstitute of Cancer Research, London, UK.
Justin ChangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Christopher J F CameronProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Noam ShoreshBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Elizabeth GaskellBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jorg DrenkowFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Jessika AdrianDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Sergey AganezovDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
François AguetBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Gabriela Balderrama-GutierrezDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
Samridhi BanskotaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Guillermo Barreto CoronaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Sora CheeLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
Surya B ChhetriHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Gabriel Conte Cortez MartinsProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Cassidy DanykoFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Carrie A DavisFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Daniel FaridProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Nina P FarrellBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Idan GabdankDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Yoel GofinDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
David U GorkinLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
Mengting GuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Vivian HechtBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Benjamin C HitzDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Robbyn IssnerBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Yunzhe JiangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Melanie KirscheDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
Xiangmeng KongProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Bonita R LamDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Shantao LiProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Bian LiProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Xiqi LiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Khine Zin LinDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Ruibang LuoDepartment of Computer Science, The University of Hong Kong, Hong Kong, CHN.
Mark MackiewiczHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Ran MengProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Jill E MooreProgram in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Jonathan MudgeEuropean Bioinformatics Institute, Cambridge, Cambridgeshire, GB.
Nicholas NelsonBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Chad NusbaumBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Ioann PopovProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Henry E PrattProgram in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Yunjiang QiuLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
Srividya RamakrishnanDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
Joe RaymondBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Leonidas SalichosProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA.
Alexandra ScavelliFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Jacob M SchreiberDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Fritz J SedlazeckDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Lei Hoon SeeFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Rachel M ShermanDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
Xu ShiProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Minyi ShiDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Cricket Alicia SloanDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
J Seth StrattanDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Zhen TanProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Forrest Y TanakaDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Anna VlasovaCentre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre, Barcelona, Spain; Institute of Research in Biomedicine, Barcelona, Spain.
Jun WangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Jonathan WernerFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Brian WilliamsDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Min XuProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Chengfei YanProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Lu YuInstitute of Cancer Research, London, UK.
Christopher ZaleskiFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Jing ZhangDepartment of Computer Science, University of California, Irvine, Irvine, CA, USA.
Kristin ArdlieBroad Institute of MIT and Harvard, Cambridge, MA, USA.
J Michael CherryDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Eric M MendenhallHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
William S NobleDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Zhiping WengProgram in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Morgan E LevineProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
Alexander DobinFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Barbara WoldDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Ali MortazaviDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
Bing RenLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
Jesse GillisFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Physiology, University of Toronto, Toronto, ON, Canada.
Richard M MyersHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Michael P SnyderDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Jyoti ChoudharyInstitute of Cancer Research, London, UK.
Aleksandar MilosavljevicDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Michael C SchatzDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. Electronic address: mschatz@cs.jhu.edu.
Bradley E BernsteinBroad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. Electronic address: Bradley_Bernstein@dfci.harvard.edu.
Roderic GuigóCentre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Universitat Pompeu Fabra, Barcelona, Catalonia, Spain. Electronic address: roderic.guigo@crg.eu.
Thomas R GingerasFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. Electronic address: gingeras@cshl.edu.
Mark GersteinSection on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA. Electronic address: mark@gersteinlab.org.
Funding
Single-Cell Biology Shared ResourceP30CA045508 · NCI · COLD SPRING HARBOR LABORATORY · PI David A Tuveson · 1987 to 2026
$118.9MBaylor College of Medicine/Stanford University Clinical Genome Resource (CLINGEN)U24HG009649 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI TERI Ellen KLEIN, Aleksandar Milosavljevic · 2021 to 2026
$31.5MA Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0MPRODUCTION CENTER FOR MAPPING REGULATORY REGIONS OF THE HUMAN GENOMEUM1HG009442 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2017 to 2021
$20.1MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MA Catalog of Cell Types and Genomic Elements in Tissues, Organoids and DiseaseUM1HG009390 · NHGRI · BROAD INSTITUTE, INC. · PI BERNSTEIN, BRADLEY EVAN · 2017 to 2021
$11.0MLandscape of transcription in human and mouseU54HG007004 · NHGRI · COLD SPRING HARBOR LABORATORY · PI GINGERAS, THOMAS RAYMOND · 2012 to 2017
$10.6MEDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4MDemocratization of Data Analysis in Life Sciences Through GalaxyU24HG006620 · NHGRI · PENNSYLVANIA STATE UNIVERSITY, THE · PI Daniel James Blankenberg, Jeremy Goecks · 2021 to 2026
$9.8MExpanding the catalog of chromatin regulatory elements in the human genomeU54HG006991 · NHGRI · BROAD INSTITUTE, INC. · PI BERNSTEIN, BRADLEY EVAN · 2012 to 2016
$7.9MNovel algorithm development, user support and maintenance for STARR01HG009318 · NHGRI · COLD SPRING HARBOR LABORATORY · PI DOBIN, ALEXANDER · 2017 to 2021
$2.4MRevealing the transcriptomic basis of neuronal identity through functional meta-analysisR01MH113005 · NIMH · COLD SPRING HARBOR LABORATORY · PI GILLIS, JESSE · 2017 to 2021
$2.4MNCI NIH HHS P30 CA045508NCI NIH HHS U01 CA253481NHGRI NIH HHS R01 HG009318NHGRI NIH HHS U24 HG006620NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24 HG009397NHGRI NIH HHS U24 HG009446NHGRI NIH HHS U24 HG009649NHGRI NIH HHS U54 HG006991NHGRI NIH HHS U54 HG007004NHGRI NIH HHS UM1 HG009390NHGRI NIH HHS UM1 HG009442NIMH NIH HHS R01 MH101814NIMH NIH HHS R01 MH113005NLM NIH HHS R01 LM012736
Abstract
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
Indexed as
EpigenomeQuantitative Trait LociGenome-Wide Association StudyGenomicsPhenotypePolymorphism, Single Nucleotideallele-specific activityENCODEeQTLsfunctional epigenomesfunctional genomicsgenome annotationsGTExpersonal genomepredictive modelsstructural variantstissue specificitytransformer model
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.